Egg, veggie, and cheese omelets baked in tortilla cups for a super convenient and fun way to have breakfast! These mini egg and cheese tortilla cups make a great make-ahead breakfast and can be frozen too.

Sunday morning brunch is one of my favorite meals of the week. I look forward to it all week and because it’s the only time we get to have breakfast together as a family, without rushing out the door that is.

Problem is that my daughter is very picky so I’m always trying to develop recipes that she can enjoy along with us. At first, I was hesitant to add peppers to the dish but I had to because they are so good in eggs. She loved these mini egg and cheese tortilla cups and so did we!

This is as easy as it can get folks. These mini egg and cheese breakfast bites are perfect for kids and adults. They are also great on the go, take them to school or work, and watch the compliments roll in!


The mixture I used to fill the tortillas is very basic yet absolutely delicious. You’re going to need some flour tortillas, any type of shredded cheese you like ( I used a mixture of cheddar and mozzarella), sour cream (you can also use heavy cream or milk), and veggies. I used a mixture of colored bell peppers and onions.


It all starts with cutting your small flour tortillas into even smaller circles. You want the circles to fit into a muffin tin without any excess tortilla popping out.

Next, simply whip the eggs and sour cream, season with salt and pepper, and pour into the prepared tortilla cups. Sprinkle with your favorite mixture of veggies and sprinkle with cheese and all that’s left to do is bake!

Easy Mini Egg and Cheese Tortilla Cups

You want to bake them until the tortilla crust is super crispy and the eggs are cooked through. If you like extra cheese, feel free to sprinkle more cheese onto them halfway through cooking.

Wanna spice it up? add some blanched broccoli, diced bacon, potato hash, or any else you would usually use in an omelet!

I advise you to make extra because these little bites will not last! my daughter literally finished half of them before they even hit the table!

4.72 from 28 votes

Mini Egg and Cheese Tortilla Cups

By: Layla
Egg, veggie, and cheese omelets baked in tortilla cups for a super convenient and fun way to have breakfast! These mini egg and cheese tortilla cups make a great make-up breakfast and can be frozen too.
Prep5 minutes
Cook15 minutes
Total20 minutes
Servings 12 tortilla cups


  • 8 eggs
  • 1/2 cup sour cream, or milk, or heavy cream
  • 1 cup shredded cheese, you can use any type, I used cheddar and mozzarella
  • diced veggies, I used a mixture of bell peppers and onions
  • 2 extra large tortilla or 8-12 small
  • salt and pepper to taste


  • Heat oven to 350 degrees F. Grease a 12 cup muffin pan and set aside.
  • Stack tortillas and cut out 12 small (about 3.5 inch) round circles out of the tortillas, you can use anything that has a rim, can, cup, bowl. If you are using big tortillas cut the four circles out of one tortilla. If you are using small tortillas you will only be able to cut one out of each tortillas. Press each wrap circle into 12 greased muffin tins using your fingers. It's okay if it doesn't fit perfectly, it will balance out after you add the eggs. Set aside.
  • In a medium bowl, whip the eggs and sour cream until fully combined, it's okay if it's a little lumpy, the sour cream will bake into the eggs. Add half of the cheese and set half aside, sprinkle salt and pepper to taste. Pour the equally into the prepared muffin tins ( into the tortillas), then sprinkle the veggies as desired.
  • Bake for 10 minutes, after 10 minutes sprinkle the rest of the cheese on the eggs, continue baking for 3-5 minutes more or until cheese is bubbly and tortilla crust is golden. Serve warm, eat using a fork or grab one and bite right in!



Serving: 1tortilla cup, Calories: 107kcal, Carbohydrates: 4g, Protein: 6g, Fat: 7g, Saturated Fat: 3g, Cholesterol: 121mg, Sodium: 143mg, Potassium: 95mg, Fiber: 1g, Sugar: 1g, Vitamin A: 670IU, Vitamin C: 16mg, Calcium: 80mg, Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Breakfast
Cuisine: American
Keyword: cheese, egg, tortilla
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  1. 4” rounds fit better. I added red bell pepper and green onions then topped with chopped fried bacon pieces. Yum!

  2. Delicious. I used 3 eggs, have to watch my carbs, diabetes demands it.
    I am going figure out the nutritional values.
    I used small corn tortillas, perfect size for my muffin pan
    Thanks for this wonderful recipe.

  3. looks very promising, however I would like to not waste any food. So do you have a very good suggestion to use the leftover tortillas pieces,,,,,,,,,,,,,,,,,,,,,being food frugal and re purposing is important to me. Always looking for new ways to stretch a dollar or food. Penny saved and all 🙂

    1. U could fry them and top with cinnamon sugar for snacking or ice cream/yogurt topping

    2. For the left over tortillas, I’m going dip them in cinnamon sugar and deep fry them for a bit. A little sweet dessert with vanilla ice cream!

  4. These are fantastic. I made these for my 5 kids aged 9-1 and they loved them. I only used 5 eggs opposed to 8 because that is all our chickens supplied us that morning, but I followed the rest of the recipe. They baked well and we’re light and airy. These will definitely be a regular in our house. I can’t wait to add pepper jack cheese and jalapeños to some, mushrooms and different types of cheeses, as well as sausage or bacon for the meat eaters in my family. The sky is the limit with these. Thank you for this recipe.

  5. Recipe says sour cream instructions say cream cheese what is correct

  6. These were just delicious!! I used low carb tortillas. These will be made often in my house!